SMTL ID : 8v9p.1

Proteus vulgaris tryptophan indole-lyase complexed with (3S)-dioxindolyl-L-alanine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 3 residues within 4Å: Chain A: G.53, N.271 Chain B: E.70 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.70, A:G.53, H2O.4, H2O.5, H2O.20 K.2: 3 residues within 4Å: Chain A: E.70 Chain B: G.53, N.271 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.70, B:G.53, H2O.4, H2O.7, H2O.20 K.6: 3 residues within 4Å: Chain C: G.53, N.271 Chain D: E.70 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: C:G.53, D:E.70, H2O.28, H2O.30, H2O.38 K.8: 3 residues within 4Å: Chain C: E.70 Chain D: G.53, N.271 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:E.70, D:G.53, H2O.30, H2O.35

4 x YQK: (2~{E})-2-[(~{Z})-[2-methyl-3-oxidanyl-5-[[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxymethyl]-1~{H}-pyridin-4-ylidene]methyl]imino-3-[(3~{S})-3-oxidanyl-2-oxidanylidene-1~{H}-indol-3-yl]propanoic acid(Non-covalent)

YQK.3: 25 residues within 4Å: Chain A: F.37, L.49, T.50, S.52, Q.99, G.100, R.101, E.104, F.132, D.133, T.134, T.135, T.190, N.194, D.223, R.226, S.263, K.265, K.266, V.389, L.395, R.414, H.458, F.459 Chain B: Y.72 36 PLIP interactions: 36 interactions with chain A Hydrophobic interactions: A:F.37, A:F.132, A:F.132, A:F.132, A:T.190, A:V.389, A:L.395 Hydrogen bonds: A:T.50, A:D.51, A:S.52, A:Q.99, A:G.100, A:R.101, A:R.101, A:D.133, A:T.135, A:N.194, A:D.223, A:R.226, A:R.226, A:S.263, A:K.266 Water bridges: A:R.101, A:T.134, A:T.135, A:A.225, A:K.265, A:K.266 Salt bridges: A:R.101, A:R.226, A:K.265, A:K.266, A:K.266, A:R.414 pi-Stacking: A:F.459, A:F.459 YQK.5: 25 residues within 4Å: Chain A: Y.72 Chain B: F.37, L.49, T.50, D.51, S.52, Q.99, G.100, R.101, E.104, F.132, D.133, T.134, T.135, T.190, N.194, D.223, R.226, S.263, K.265, K.266, V.389, L.395, R.414, F.459 33 PLIP interactions: 32 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.37, B:F.132, B:T.190, B:V.389, B:L.395 Hydrogen bonds: B:T.50, B:T.50, B:S.52, B:Q.99, B:G.100, B:R.101, B:R.101, B:D.133, B:N.194, B:D.223, B:R.226, B:R.226, B:S.263, B:K.266 Water bridges: B:R.101, B:T.134, B:T.134, B:A.225, B:K.265, A:Y.72 Salt bridges: B:R.101, B:R.226, B:K.265, B:K.266, B:K.266, B:R.414 pi-Stacking: B:F.459, B:F.459 YQK.7: 25 residues within 4Å: Chain C: F.37, L.49, T.50, S.52, Q.99, G.100, R.101, E.104, F.132, D.133, T.134, T.135, T.190, N.194, D.223, R.226, S.263, K.265, K.266, V.389, L.395, R.414, H.458, F.459 Chain D: Y.72 32 PLIP interactions: 32 interactions with chain C Hydrophobic interactions: C:F.37, C:F.132, C:F.132, C:T.190, C:V.389, C:L.395 Hydrogen bonds: C:S.52, C:Q.99, C:G.100, C:R.101, C:R.101, C:D.133, C:T.134, C:N.194, C:D.223, C:R.226, C:R.226, C:S.263, C:K.266 Water bridges: C:R.101, C:T.134, C:T.134, C:K.265, C:K.266 Salt bridges: C:R.101, C:R.226, C:K.265, C:K.266, C:K.266, C:R.414 pi-Stacking: C:F.459, C:F.459 YQK.9: 25 residues within 4Å: Chain C: Y.72 Chain D: F.37, L.49, T.50, D.51, S.52, Q.99, G.100, R.101, E.104, F.132, D.133, T.134, T.135, T.190, N.194, D.223, R.226, S.263, K.265, K.266, V.389, L.395, R.414, F.459 34 PLIP interactions: 34 interactions with chain D Hydrophobic interactions: D:F.37, D:F.132, D:F.132, D:T.190, D:V.389, D:L.395 Hydrogen bonds: D:T.50, D:T.50, D:D.51, D:S.52, D:Q.99, D:G.100, D:R.101, D:R.101, D:D.133, D:T.135, D:N.194, D:D.223, D:R.226, D:R.226, D:S.263, D:K.266 Water bridges: D:T.134, D:T.134, D:A.225, D:K.265, D:K.266 Salt bridges: D:R.101, D:R.226, D:K.265, D:K.266, D:K.266, D:R.414 pi-Stacking: D:F.459

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 2 residues within 4Å: Chain B: K.333, Y.348 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.340, B:Y.348 Salt bridges: B:D.337

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Phillips, R.S., Proteus vulgaris tryptophan indole-lyase complexed with L-ethionine. To Be Published

Release Date

2023-12-20

Peptides

Tryptophanase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Tryptophanase

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